Dear Amber users,
I'm currently interested in the simulation of a system composed by two bilayers separated by a water slab between those two bilayers and with water slabs on the simulation cell boundaries. As I intend to use LIPID11, a surface tension dependent FF for this system, I believe that the ninterface value should be adjusted accordingly to the number of water/lipid interfaces, following the statement on page 26 of the AMBER12 manual:
ninterface
Number of interfaces in the periodic box. There must be at least two interfaces in the periodic box. Two interfaces is appropriate for a lipid bilayer system and is the default value.
So, if for a single bilayer system ninterface = 2, then for a double bilayer system ninterface = 4. What are your thoughts concerning this change?
I am yet to discover if the surface tension value should be changed from the value appropriate for a single bilayer system.
Regards,
JM
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 16 2012 - 04:00:03 PDT
